2011
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions
Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science 2011, 20: 1745-1754. PMID: 21826754, PMCID: PMC3218368, DOI: 10.1002/pro.710.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyDatabases, ProteinModels, MolecularProtein BindingProtein Interaction MappingProteinsSoftwareConceptsMulti-interface hubsMolecular networksConformational changesInteraction networksTransient interactionsStructural interaction networksProtein interaction networksClassification of proteinsDynamic conformational changesProtein structural featuresSmall conformational changesTransient associationGene expressionMore plasticityProtein motionsStructural databankProteinAlternate conformationDifferent mechanismsDrastic structural changesDomainInteraction
2009
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes
Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins Structure Function And Bioinformatics 2009, 78: 309-324. PMID: 19705487, DOI: 10.1002/prot.22544.Peer-Reviewed Original ResearchConceptsLarge macromolecular complexesMacromolecular complexesLarge-scale conformational changesRNA polymerase IIT7 RNA polymeraseMultiple polypeptide chainsPolymerase IIRNA polymeraseDistance conservationPhosphate dikinaseDifferent conformationsInter-residue distancesLarge complexesConformational changesPolypeptide chainDomain motionPartial refoldingFurther distinguishing featureConformationStructure determinationComplexesDikinaseSensitive identificationGroELIdentification
2008
An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces
Abyzov A, Uzun A, Strauss P, Ilyin V. An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces. PLOS Computational Biology 2008, 4: e1000066. PMID: 18437203, PMCID: PMC2289873, DOI: 10.1371/journal.pcbi.1000066.Peer-Reviewed Original Research
2007
UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinB
Godoy V, Jarosz D, Simon S, Abyzov A, Ilyin V, Walker G. UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinB. Molecular Cell 2007, 28: 1058-1070. PMID: 18158902, PMCID: PMC2265384, DOI: 10.1016/j.molcel.2007.10.025.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesBlotting, Far-WesternDNA Polymerase betaDNA-Directed DNA PolymeraseEscherichia coliEscherichia coli ProteinsModels, MolecularMolecular Sequence DataMutagenesisMutationProtein BindingProtein Structure, TertiaryRec A RecombinasesSequence Homology, Amino AcidConceptsRegulatory protein-protein interactionsDNA damage-inducible proteinProtein-protein interactionsY-family DNA polymerasesFamily DNA polymerasesMutagenic phenotypeOpen active siteDinBRecAMutagenic potentialDNA polymeraseFrameshift mutagenesisProteinStructural modelingActive siteEukaryotesOrthologsArchaeaUmuDMutagenesisPolymerasePhenotypeBacteriaSitesEvolution
2005
ACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICS
SHEHADI I, ABYZOV A, UZUN A, WEI Y, MURGA L, ILYIN V, ONDRECHEN M. ACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICS. Journal Of Bioinformatics And Computational Biology 2005, 3: 127-143. PMID: 15751116, DOI: 10.1142/s0219720005000916.Peer-Reviewed Original Research